Saturday, February 27, 2010

In many parts of the world, obtaining clean drinking water is a daily struggle. As many as a billion people may lack access to clean water. Modern purification methods are often too expensive for the poorest communities to implement. For this reason, simpler and cheaper water purification methods are in great need. Habauka Kwaambwa of the University of Botswana and his colleagues have found a novel first step in water purification.

Before water can be drunk, it must go through several stages of purification. The first step, flocculation, removes large particulates from the water. Later steps include filtration and disinfection. Aluminum or iron salts are commonly used for flocculation, but Kwaambwa has found that extracts from Moringa oleifera tree seeds can work just as well.

Moringa oleifera trees are native to India, but cultivated in Africa, South America and many other parts of the world. Almost every part of them can be eaten or used in some manner. Now, they may even play an important role in water purification.

Moringa oleifera tree cultivated in village of Antanimieva, southwestern Madagascar, taken by Mark E. Olsen, 1998.

Friday, February 26, 2010

Researchers from the University of Missouri have developed a way to detect malignant melanoma cells in lymph nodes.

Melanoma is a deadly and fast growing form of skin cancer. There are different melanoma classification systems that rely on depth of penetration of the tumor and areas affected, but here’s a typical example from The Melanoma Center:

Stage 0: the melanoma is in the outer layers of skin

Stage I: the melanoma has reached the inner layers of skin but is small

Stage II: the melanoma is larger and has spread throughout the skin layers but has not metastasized

Stage III: the melanoma has spread to the lymph nodes

Stage IV: the melanoma is found throughout the body.

Once a tumor reaches the lymph nodes, entirely different treatment options are needed. Therefore, it’s critical to be able to distinguish Stage II melanomas from Stage III. John Viator and his team are using photoacoustics (laser-induced sound) to do just that.

They injected human melanoma cells into dog and pig lymph nodes and scanned the nodes with their laser. The melanoma cells, containing melanin, react to the scan by absorbing the light. The absorbed light causes the cells to rapidly heat and expand, followed by immediate cooling and contraction. This results in a popping noise that can be detected by special instruments.

Rather than having to examine every cell within a biopsied lymph node, a Herculean task, this technique will allow doctors to determine whether melanoma cells are present, and if so, where.

This procedure has not yet been tried on human patients, but the doctors are hopeful that clinical trials will prove its efficacy.

Wednesday, February 24, 2010

William Martin, from the Institut für Botanik III Heinrich-Heine-Universität, Düsseldorf, Germany and colleagues from the University of London, have a new theory about the origin of life. Rather than having arisen out of a ‘primordial soup’ a theory first published by J.B.S. Haldane in 1929, they believe life arose from gases around deep-sea hydrothermal vents.

The idea that life evolved at the base of hydrothermal vents was proposed by Michael J. Russell of the Jet Propulsion Laboratory, Caltech. Tiny crevasses in the deep sea vents enclose micro-environments containing mixes of H2, CO2, N2, and H2S which could have recombined into organic molecules.

Geochemical gradients across the tiny pores in these microscopic caverns could have driven energy production. This ‘proton-motive force’, also known as chemiosmosis, may have allowed the earliest cells to generate adenosine triphosphate (ATP) or an equivalent energy currency. Martin and his team suggest that the external protein gradient of the vent pores was replicated within the earliest cells.

There are two reasons to suspect that Martin and his team are on to something. For one thing, there are creatures alive today that rely on hydrothermal energy rather than on the sun. So, clearly it’s possible for organisms to make their living in this way. For another, most extant organisms use a similar internal ion gradient to synthesize ATP.

Martin argues that the reason living organisms employ chemiosmosis is that their earliest ancestors did as well.

Tuesday, February 23, 2010

Watching the Olympics has put me in the mood for a story about concussions.

Concussion, or mild traumatic brain injury, is a common problem for athletes. Briefly, concussion is a bruised brain. It occurs when the brain slams against the inside of the skull following rapid deceleration or impact. Symptoms can include headache, visual problems, nausea, convulsions, disorientation and unconsciousness. Because of the great range of symptoms, it can be difficult to assess whether an athlete has suffered a concussion. This knowledge is critical, as suffering a second concussion before the first has healed can have catastrophic effects, particularly for children.

James Eckner of the University of Michigan has devised a quick and simple method of assessing whether an athlete has in fact suffered a concussion, based on an idea by Michigan high school student Ian Richardson. The researchers plan to present their idea at a meeting of the American Academy of Neurology in the spring.

Eckner and his team attached a hockey puck to the bottom of a stick containing centimeter markings along its length. During the test, the researcher suddenly releases the stick, and the patient is asked to grab it as quickly as he can. The markings indicate how far the stick travels before the patient catches it.

James Eckner tests the reaction time of one of the study's authors, James Richardson, using the method they developed. University of Michigan.

Eckner compared the reaction times of 8 college football players both before and after they had had independently diagnosed concussions (192 students did not have concussions, so could not be used for the latter part of the study). The post-concussion reaction times were about 15% slower (30 milliseconds).

Dr. Eckner cautions that this was only a preliminary test, and should be repeated with larger numbers of subjects. In addition, it should be tested under a variety of field conditions. Although coaches and medical teams may bring the weighted stick to games, they won’t necessarily have tables and chairs at the ready. If the device does prove to be reliable, the researchers suggest that it be used as a screening tool to assess whether athletes should be allowed back into play.

Monday, February 22, 2010

Nir Eynon and his colleagues at the Wingate Institute, plus Alberto Alves from the University of Porto, compared elite endurance runners (who had competed internationally) with long distance runners who had only competed nationally, sprinters, and healthy non-athletes. In particular, the researchers were looking at the ‘nuclear respiratory factor 2’ (NRF2) gene, which encodes a mitochondrialtranscription factor. In other words, our cells’ power plants depend on NRF2. In addition, NRF2 is thought to be involved in mitigating exercise induced oxidation and inflammation.

The scientists found that a particular NRF2 allele occurred much more frequently in elite endurance runners than in sprinters (80% of the time, vs. 46% of the time). This particular gene did not differ significantly between the sprinters and the non-competitive controls.

Perhaps one day, athletes will choose their distances based on their genetic make up.

Sunday, February 21, 2010

Locked-in syndrome is a tragic condition in which a brain injury robs a person of the ability to move or communicate in any way. Often doctors and family members cannot ascertain whether the patient is aware at all, or is completely vegetative. In the cases where doctors suspect that the patient is at least partially conscious of his surroundings, it has been a frustrating struggle to try to find ways to communicate with the patient.

Recently, Adrian Owen of Cambridge, Steven Laureys of the University of Liège in Belgium, and other neurologists may have found a key to locked-in syndrome.

The doctors performed functional magnetic resonance imaging (fMRI) scans of 54 patients who were in either a vegetative state (no apparent awareness) or a minimally conscious state (occasional episodes of cognitive behavior). None of the patients had been able to communicate prior to these experiments. While hooked up to the scanners, the patients were asked to imagine themselves playing tennis, or walking around their own apartments. Because these two scenarios were expected to activate different parts of their brains, the doctors hoped they would able to detect whether the patients were in fact aware.

Five of the patients were able to understand the instructions and conjure up the correct images in their minds, as seen by the scans. One patient was even able to use the fMRI system to communicate. By thinking of playing tennis for ‘yes’ and walking around the apartment for ‘no’, he was able to answer a series of questions.

Although this technique is impractical for any meaningful two-way communication, it could be used to assess the consciousness of locked-in patients. I believe it was suggested on The Skeptics’ Guide to the Universe that patients might also be able to take greater charge of their own care by indicating whether they approved of certain procedures.

Saturday, February 20, 2010

Heart surgery patients often require plasma transfusions. About one in every 3000 transfusions results in an extremely dangerous condition called ‘transfusion-related acute lung injury' (TRALI). There is some evidence that TRALI is linked to plasma that was donated by females. TRALI is thought to be an immune reaction, and female mammals, particularly ones who have been pregnant, contain antibodies to certain cell surface factors. Briefly, it was thought that the female antibodies were triggering a catastrophic immune reaction.

For this reason, in 2006 the AABB (formerly the American Association of Blood Banks) recommended that blood banks avoid using plasma from female donors.

Three years later, Mark Stafford-Smith and his team from Duke University Medical Center tested whether that advice was sound.

Even prior to the 2006 finding, the blood products from male and female donors have been kept separate. Stafford-Smith took advantage of this fact to search the records for cardiac patients who had been transfused with either female-only or male-only plasma. He identified 390 matched pairs. To his surprise, the female-only recipients actually had better outcomes. Although the long-term survival rates were similar, the female-only patients had just over half as many incidents of pulmonary dysfunction, death within 30 days of surgery, or extended hospitalization (more than ten days).

Meanwhile, female-plasma is still associated with TRALI. The researchers speculated that because TRALI is so rare, the negative effects of female plasma were overshadowed by the unexpected and thus far unexplained benefits.

To be clear, it’s the blood donors that were separated by gender, not the heart patients. This study did not distinguish between male or female patients who had been given male or female blood plasma, something I personally would have liked to see done. Also, the study only included heart patients. The doctors agree that more research is required before revising the current AABB recommendations. If the benefits of receiving female plasma can be more clearly understood and separated from the risks, this will be a boon for anyone requiring transfusion.

Friday, February 19, 2010

Julie Greer and Dongchan Jang, both from the California Institute of Technology (Caltech), have devised a novel set of materials with great strength and flexibility. How did they do this? By making things smaller….much smaller.

The building materials in use today all have advantages and disadvantages. Ceramics are very strong, but heavy and brittle. Metals can be pliable, but aren’t as strong as ceramics. One promising class of materials are called ‘glassy metallic alloys’. Glass is an amorphous solid material. In other words, glass is a material that has been cooled to its solid state without crystallizing, but instead while maintaining the liquid-like flow of atoms.

Like glass, glassy metallic alloys are also amorphous, non-crystalline solids, but containing metallic elements such as zirconium, titanium, copper, or nickel. Like true metals, they’re lightweight, and like ceramics they’re very strong. Unfortunately, also like ceramics and regular glass, they are extremely brittle.

In order to circumvent this problem, Greer and Jang designed ‘nanopillars’ of zirconium-rich glassy alloy only 100 nanometers in diameter (for reference a human hair is about 100 micrometers across). Surprisingly, these tiny pillars were both ductile and strong, making them excellent building materials. Or at least, they would be if anyone could figure out how to combine them into normal sized structures.

Greer is confident that this will happen soon:

Our findings provide a powerful foundation for utilizing nanoscale components, which are capable of sustaining very high loads without exhibiting catastrophic failure, in bulk-scale structural applications specifically by incorporating architectural and microstructural control.

Thursday, February 18, 2010

Radiocarbon dating is an extremely useful tool for archeologists or for paleontologists who work on the not too distant past.

All living things on earth contain carbon. Atmospheric carbon in the form of carbon dioxide is incorporated into plants during photosynthesis, and then consumed by animals. Most of that carbon is in the stable form carbon-12 (12C). However, there is a trace amount of radioactive carbon-14 (14C) in the atmosphere as well. While the organism is alive, both isotopes are being incorporated into the tissue at a ratio that matches that found in the atmosphere. Once the organism dies, no more 14C can be absorbed and the 14C that was there decays into nitrogen (14N). The half-life of 14C is just under 6000 years. In other words, in 6000 years, half the 14C that was in the specimen is gone, in 12,000 years, 3/4 is gone, etc. Once you get past about 50,000 years, the amount of 14C left is so small that no more meaningful data can be obtained.

This means that once you find a fossil, you can use the ratio of 12C to 14C in that fossil to determine how long ago the organism lived. There’s just one problem. You have to know the starting ratio of 12C to 14C in the atmosphere at the time the organism lived in order to assess what percentage of the radioactive carbon has decayed. Unfortunately, the amount of 14C in the atmosphere is not constant over time, but varies with fluctuations in both the Earth’s magnetic field and in the amount of solar activity. Therefore, the raw data must be corrected against a calibration curve that accounts for these fluctuations.

This is where an international group called INTCAL comes in. INTCAL has spent the past thirty years calibrating and perfecting the radiocarbon calibration curve. In 2004, by using data from tree rings and corals, the team reached consensus on a curve reaching back to 26,000 years ago. This curve was dubbed INTCAL04. More recently, the researchers have been able to extend that curve all the way to 50,000 years ago with their new INTCAL09 curve, which is published in the journal Radiocarbon.

Although carbon dating is useless for dating dinosaur fossils or other ancient life forms, it is an invaluable tool in dating early human cultures. For example, we now have a more accurate picture of when humans began painting caves, or when we migrated into Europe.

Lead author Paula Reimer of Queen’s University Belfast in Northern Ireland says they will continue to perfect the curve, and hope to have a new edition in 2011.

Tuesday, February 16, 2010

Some kinds of bacteria have been known to congregate into ‘biofilms’. Normally, free swimming bacteria which are susceptible to antibiotics and other treatments become remarkably resilient. They stick to surfaces with remarkable tenacity and are exceedingly difficult to kill. In addition, they sometimes produce toxins not made by their planktonic kin.

The viral biofilms appear to serve the same function as their bacterial counterparts, namely to offer increased infectivity and protection from the immune system. Removing the viral biofilm from infected cell surfaces reduced infection rates by up to 80%.

Although it is not yet known whether other types of viruses can form these aggregates, scientists are hopeful that this new data will open up new anti-viral treatments that target biofilms.

Monday, February 15, 2010

There have been 90 elements found in nature. Some two dozen more have been created in labs. Most of these are so transitory they exist barely long enough for researchers to take note of the fact that they were created. However, some scientists believe that there is an island of stability in super heavy elements yet to be found.

To test this hypothesis, scientists needed to accurately measure the atomic mass of a super heavy element. By determining the exact mass of the element, the binding energy can be calculated, which in turn tells how stable the element can be, and leads to predictions of even larger stable elements. Up to this point, binding energies had only been inferred from decay rates.

Nobelium (element 102) was chosen for this purpose and produced by firing calcium ions onto lead foil with a particle accelerator. Michael Block and his international colleagues used the SHIP (Separator for Heavy Ion reaction Products) filter to separate out the nobelium ions, which were then sent on through the ‘Shiptrap’ facility to trap the ions and measure their atomic mass.

This experiment yielded two firsts: the first time a super heavy element had been trapped, and the first time the atomic mass of a super heavy element had been measured with extreme accuracy (the error rate was estimated to be about 5 millionths of one percent).

Sunday, February 14, 2010

One of the things I love about science is the variety of questions it can answer. It’s really amazing how varied people’s interests are, and how creative they can be in finding answers. For example, Norman Heglund, from the Université Catholique de Louvain, Belgium, wondered whether charging elephants were truly running, or just speed walking.

Walking and running are actually two very different motions. Although both gaits convert potential energy stored in tendons and muscles into kinetic energy that moves the animal forward, the two movement patterns are quite dissimilar. Running animals use the stored energy to bounce forward like a pogo stick, whereas walking animals regain that stored energy by swinging their legs like a pendulum. Think of the bouncing, flexing backbone of a running dog, versus the more level backbone of the same dog when walking. Previous experiments by John Hutchinson of the Royal Veterinary College of London, indicated that elephants do not run at higher speeds but in fact simply walk faster.

Heglund wanted to test this hypothesis. Not having access to elephants in Belgium, he traveled to the Thai Elephant Conservation Centre in Lampang, Thailand, where he and his colleagues built a giant force-measuring platform. This eight meter long racetrack was made of one meter square force plates over a reinforced concrete foundation. Thirty-four elephants of assorted ages and weights were encouraged to cross the platform at speeds ranging from strolling to racing.

So, were the elephants running or walking when reaching top speeds? A little of both, it turns out. Although the elephants’ kinetic and potential energy plots resembled those of running animals, their centers of mass remained level during the first part of the stride, but bounced during the second part. It seemed as though the elephants were running with their front legs but walking with their hind legs.

Despite this, the researchers found that elephants are highly efficient movers, using 1/3 the energy of most other animals. Elephants achieve this efficiency by having a high step frequency and maintaining at least two feet on the ground at all times, limiting the bouncing motion most animals experience at high speeds.

Saturday, February 13, 2010

Mathieu Destribats, Véronique Schmitt and Rénal Backov of the Paul Pascal Research Center in Bordeaux have patented their design for smart capsules that release their contents at specific temperatures.

The current manner of manufacturing medicinal capsules is to place the therapeutic agent within a silica shell. This shell either has tiny pores through which the medicine can slowly escape, or the entire shell is designed to dissolve. However, neither process can be precisely controlled.

The researchers in this study have invented a novel capsule manufacturing process. Their capsules consist of the therapeutic agent mixed with oil with a specific melting temperature. When placed in water, the oil solidifies into droplets. These oil drops are then encapsulated in a silica shell. When the capsules are heated above the melting temperature of the oil, the oil expands, breaking open the silica shell and releasing the contents.

Oils can be carefully selected depending on how the agent is to be stored and/or used. Some typical melting points for oils and waxes:

olive oil: –6 °C or 21 °F

peanut oil: 3 °C or 37 °F

coconut oil: 25 °C or 77 °F

palm oil: 35 °C or 95 °F

beeswax: 62-65 °C or 144-149 °F

carnauba wax: 78-85 °C or 172-185 °F

Although this method would not work for time-released medicines (if the capsules released at all, this would happen instantly upon entering the body), it could prove useful for storing medicines. Alternatively, the capsules could be heated in a person’s hands before applying the contents to the skin. The authors also suggest that capsules containing bacteriocides could be placed in potential areas of contamination, such as air ducts, to release their contents when the spaces reached bacterial growth-friendly temperatures.

Friday, February 12, 2010

Home computers are becoming more and more common. They have tremendous processing power, but spend a large part of their time idly twiddling their bytes. In 1995, the Search for Extraterrestrial Intelligence (SETI) institute a team of astronomers from the University of Washington and UC Berkeley Space Science Lab*got the idea of harnessing that processing power. Starting in 1999, volunteers could allow SETI to ‘borrow’ their computers during idle moments to analyze chunks of data in the hopes of finding intelligent signals from space. This popular program, known as SETI@home, ran until 2005 when it was switched over to a new software platform called Berkeley Open Infrastructure for Network Computing (BOINC). The new and improved SETI@home still uses BOINC today.

Besides finding aliens, BOINC is being used for many other huge computational problems. For instance, MilkyWay@home, which was started in 2006 by Rensselaer Polytechnic Institute researchers, uses personal computers to map the Milky Way and neighboring galaxies. MilkyWay@home is currently the largest shared computer project, having surpassed SETI@home.

If you like the idea of doing your part for science but aren’t that interested in astronomy, BOINC has projects in mathematics, biology, chemistry, and other fields. And more are being started all the time. For example, the DNA@Home platform is being developed to find gene regulations sites on human DNA.

If you’re interested in signing up your computer for one of the BOINC projects, you can find the complete list here.*I attended a talk by Seth Shostak, executive director of SETI, on 2/14/2010, in which he informed me that SETI@home is not a SETI project, but is in fact a UC Berkeley program.

4.Genome studies of copy number variants (CNV). Autism-associated CNV’s tend to turn up in genes associated with neural adherence and connection, and/or genes associated with the ubiquitin pathway (among other things, involved in the turnover of synaptic products).

5.Combined therapies. Using a mix of medical (such as risperidone, an anti-psychotic drug) and behavioral therapy has been tested.

7.Mitochondrial dysfunction. Some patients with mitochondrial disorders are at increased risk for autistic regression, particularly after having a fever. (As an aside, the researchers looked for a connection with recent vaccination and did not find any correlation. This can be added to the long list of studies that have shown a complete lack of association between autism and vaccination.)

8.Late language development. Autistic children have been able to learn to speak starting as late as 12 years old.

10. Autoimmune diseases. A family history of type-1 diabetes or of rheumatoid arthritis in the mother were linked to autism in the offspring. The immune system of the mother during pregnancy may be implicated.

Wednesday, February 10, 2010

Grateful Dead percussionist Mickey Hart is working on a musical project called ‘Rhythms of the Universe’, whose intent is to ‘sonify’ the universe. To that end, he collaborated with George Smoot and Keith Jackson, both from the Lawrence Berkeley National Laboratory, to translate electromagnetic data coming from a supernova into music.

Tuesday, February 9, 2010

Filed under medical treatments I did not want to know about and certainly did not want to post a picture of:

Lucilia sericata(green bottle fly maggots) have been used since ancient times to clean and heal wounds.The practice was revived in the 1990’s, and is now relatively common, going under the name Maggot Debridement Therapy (MDT). The maggots ingest only necrotic (dead) tissue, effectively cleaning wounds.At the same time, they promote healing and reduce inflammation by secreting antimicrobial compounds into the wound.

Unfortunately, maggots infected with the bacteriaPseudomonas aeruginosadie without completing their wound care tasks. Anders Schou Andersen and his team from the University of Copenhagen in Denmark showed that the inter-bacterial communication system known as 'quorum sensing' was indirectly responsible for the maggot deaths.

Quorum sensing allows bacteria to converge into ‘biofilms’, sheets of cells that stick to surfaces and are exceeding difficult to kill. These bacterial conglomerations also produce potent toxins that kill maggots and other organisms.

When the scientists used genetically modified Pseudomonas without a functional quorum sensing system, the maggots were much less susceptible to the bacteria.It is important to note that the researchers did not protect the maggots by chemically blocking bacterial signaling, but rather relied on mutant bacteria for their tests.The bacteria that patients are likely to encounter during treatment would almost certainly have wild-type (normal) quorum sensing. In order to ensure that MDT is successful, doctors will have to first rid the wound site of pathogenic bacteria, which isn’t always an easy task.

Monday, February 8, 2010

Optical coherence tomography (OCT) is an imaging technique that uses low intensity near-infrared light to make cross-sectional pictures. It is commonly used to take pictures of the retina and other tissues.

Normally, most of the light shining on an object ends up scattering off in all directions. Only a fraction of the light reflects off structures beneath the surface of the object. OCT filters out the scattered glare, detecting only the reflected light. The technique, which can be likened to an optical ultrasound, can be used to build up a layered picture of biological tissue up to 2 mm deep.

OCT has also been used to exam art objects such as oil paintings. For those of you who know as little about art as I do, oil paintings are made up of many separate layers. Today, gesso is usually applied first as a primer, in earlier times glue made from animal hides was used. On top of that, the artist may use a variety of layers including sketches or outlines, multiple coats of paint, glazes and varnish. The artist will usually add a signature or other inscription as one of the last touches.

Piotr Targowski and his team from Nicolaus Copernicus University, Poland, have used OCT to examine two oil paintings, putatively from the 18th and 19th centuries. The researchers determined in which order various inscriptions and paint layers had been laid down on the canvases. With this information, they could more accurately determine the first painting’s date of creation. Perhaps more importantly, the timing of the layers strongly suggested that the artist’s signature on the second painting was a forgery.

Stochastic Scientist? What's up with that?

Why the Stochastic Scientist? As I'm sure you all know, 'stochastic' is another word for 'random', which is what I intend for the focus of this blog. Although my formal training is as a molecular biologist, there are many other fields of science that are also fascinating and beautiful. It's my intention to blog about which ever scientific discovery or invention catches my, and hopefully your, fancy.

I also hope to inspire people to learn more about science. By choosing among a huge variety of scientific endeavors, I'll undoubtably hit upon something that will pique my readers' interest.

I guess I could have called my blog 'The Joy of Science', but that wouldn't have been quite so random.